title: Thermal adaptation of conformational dynamics in ribonuclease H.
abstract: The relationship between inherent internal conformational processes and enzymatic activity or thermodynamic stability of proteins has proven difficult to characterize. The study of homologous proteins with differing thermostabilities offers an especially useful approach for understanding the functional aspects of conformational dynamics. In particular, ribonuclease HI (RNase H), an 18 kD globular protein that hydrolyzes the RNA strand of RNA:DNA hybrid substrates, has been extensively studied by NMR spectroscopy to characterize the differences in dynamics between homologs from the mesophilic organism E. coli and the thermophilic organism T. thermophilus. Herein, molecular dynamics simulations are reported for five homologous RNase H proteins of varying thermostabilities and enzymatic activities from organisms of markedly different preferred growth temperatures. For the E. coli and T. thermophilus proteins, strong agreement is obtained between simulated and experimental values for NMR order parameters and for dynamically averaged chemical shifts, suggesting that these simulations can be a productive platform for predicting the effects of individual amino acid residues on dynamic behavior. Analyses of the simulations reveal that a single residue differentiates between two different and otherwise conserved dynamic processes in a region of the protein known to form part of the substrate-binding interface. Additional key residues within these two categories are identified through the temperature-dependence of these conformational processes.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America.
authors.forename: Kate A
authors.initials: KA
authors.lastname: Stafford
authors.forename: Paul
authors.initials: P
authors.lastname: Robustelli
authors.forename: Arthur G
authors.initials: AG
authors.lastname: Palmer
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D025341:Principal Component Analysis; D011485:Protein Binding; D011487:Protein Conformation; D016914:Ribonuclease H / Q000737:chemistry* / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D016914:Ribonuclease H; C078856:ribonuclease HI